Designated Villain: The murderous duo that the protagonists chase. The reader sympathises with their attempts to free humanity by killing the Old Ones. Unusually for this trope, the YMMV aspect is that some readers would debate whether or not the murderous duos were designated as the villain of the piece, or if they were intended to be the heroes.
Since Holmes is implied to be trying to develop nuclear weapons (and if anyone can pull off a one-man Manhattan Project it's Holmes) he'll likely be integral to the success of the ultimate revolution. The real question, though, is whether they can manage to avoid the collapse of the 'Soviet Union' or make a sensible Detente with the Eldritch Horrors.
Sherry Vernet. An offhand comment by Holmes is that his grandmother was the sister of an artist named Vernet.
Readers who are particularly knowledgable about Sherlock Holmes will realize earlier the protagonists' real identities as Moran and Moriarty.
It's pretty common for professionally published pastiches to write around trademarks by leaving characters unnamed, so the narrator only referring to the detective as "my friend" is unsurprising. Thus putting the audience off from the REAL reason that they remain unnamed until the end.
The advert at the start of chapter 4 claims that V. Tepes can help you if you are feeling quinsy. This might be a reference to Quincy Morris, a character from Dracula who often gets Adapted Out.
Nightmare Fuel: The narrator's description of his encounter with an Eldritch Abomination which maimed him, killed every other soldier present and left him extremely traumatised.